If a coil is not firing, the head pipe temps will be cold; 2/3 or 1/4. If you still have the 4 into 4s you can feel the exhaust to find dead cylinders.
IMO, you still need to look at the spark plug tips. The deposits are the best indicator for combustion conditions. If you have a spare set of plugs, swap them and see if the trouble persists. If so, you eliminated a possibility. If not, new plugs are an easy fix.
1000 miles ago the engine ran well. Now it doesn't. To me, that means all the tune up items need to be addressed, as these items can easily make the engine run poorly. You don't have to replace anything unless a check shows it needs to be done. Timing can change/slip, and points can burn if the ignition is left on without the bike running.
The tank should have a fuel filter above the fuel tap. If your tank is clean, it's either well preserved or it has been cleaned. If cleaned, by who, and did the retain the stock filter intact. Clearly, clean carbs fed dirty fuel won't remain clean very long. And, the pilot jets only need a .016" sized peice of sediment to block them.
If the paper air filter got wet, the fibers collapse, and this chokes the engine. The plugs can get soot deposits, and short out. One reason to look at the plugs. White plugs are an indication of fuel starvation. A cold engine needs fuel enrichment, a hot engine doesn't.
I was just trying to gather information to help you. If you don't share information we've asked for, it looks as though you are just taking discussion with those in agreement with your a theories.
Best of luck!